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Bioinformatics. 2005 Feb 1;21(3):402-4. Epub 2004 Sep 7.

SNAP: workbench management tool for evolutionary population genetic analysis.

Author information

  • 1Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.

Abstract

The reconstruction of population processes from DNA sequence variation requires the coordinated implementation of several coalescent-based methods, each bound by specific assumptions and limitations. In practice, the application of these coalescent-based methods for parameter estimation is difficult because they make strict assumptions that must be verified a priori and their parameter-rich nature makes the estimation of all model parameters very complex and computationally intensive. A further complication is their distribution as console applications that require the user to navigate through console menus or specify complex command-line arguments. To facilitate the implementation of these coalescent-based tools we developed SNAP Workbench, a Java program that manages and coordinates a series of programs. The workbench enhances population parameter estimation by ensuring that the assumptions and program limitations of each method are met and by providing a step-by-step methodology for examining population processes that integrates both summary-statistic methods and coalescent-based population genetic models.

AVAILABILITY:

SNAP Workbench is freely available at http://snap.cifr.ncsu.edu. The workbench and tools can be downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset.

SUPPLEMENTARY INFORMATION:

A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu.

PMID:
15353448
[PubMed - indexed for MEDLINE]
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